Hybrid spatial Gillespie and particle tracking simulation | Zendy

Michael Klann | Zendy; Arnab Ganguly | Zendy; Heinz Koeppl | Zendy

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Hybrid spatial Gillespie and particle tracking simulation

Author(s) -

Michael Klann,

Arnab Ganguly,

Heinz Koeppl

Publication year - 2012

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/bts384

Subject(s) - computer science , cluster analysis , stochastic simulation , brownian motion , tracking (education) , brownian dynamics , signal (programming language) , statistical physics , particle (ecology) , biological system , algorithm , simulation , artificial intelligence , physics , statistics , mathematics , biology , ecology , psychology , programming language , pedagogy

Cellular signal transduction involves spatial-temporal dynamics and often stochastic effects due to the low particle abundance of some molecular species. Others can, however, be of high abundances. Such a system can be simulated either with the spatial Gillespie/Stochastic Simulation Algorithm (SSA) or Brownian/Smoluchowski dynamics if space and stochasticity are important. To combine the accuracy of particle-based methods with the superior performance of the SSA, we suggest a hybrid simulation.

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